null Sun 23 Dec 22:22:59 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pg4-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-4.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-4.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:09 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-4.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6705 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.54 Input MTZ file: 2pg4-4.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 77.669 4.000 Wilson plot Bfac: 92.45 2116 reflections ( 99.39 % complete ) and 0 restraints for refining 1692 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3851 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3515 (Rfree = 0.000) for 1692 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.06 3.85 Search for helices and strands: 0 residues in 0 chains, 1737 seeds are put forward NCS extension: 0 residues added, 1737 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 7 peptides. Score 0.225 Round 2: 70 peptides, 14 chains. Longest chain 10 peptides. Score 0.290 Round 3: 79 peptides, 12 chains. Longest chain 11 peptides. Score 0.427 Round 4: 86 peptides, 12 chains. Longest chain 15 peptides. Score 0.476 Round 5: 88 peptides, 10 chains. Longest chain 15 peptides. Score 0.548 Taking the results from Round 5 Chains 10, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3384 restraints for refining 1373 atoms. 3082 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3547 (Rfree = 0.000) for 1373 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 2: After refmac, R = 0.3106 (Rfree = 0.000) for 1351 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2743 (Rfree = 0.000) for 1338 atoms. Found 2 (6 requested) and removed 8 (3 requested) atoms. Cycle 4: After refmac, R = 0.2673 (Rfree = 0.000) for 1323 atoms. Found 0 (6 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2590 (Rfree = 0.000) for 1307 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.84 3.64 Search for helices and strands: 0 residues in 0 chains, 1361 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1382 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.306 Round 2: 80 peptides, 13 chains. Longest chain 9 peptides. Score 0.402 Round 3: 75 peptides, 12 chains. Longest chain 10 peptides. Score 0.398 Round 4: 79 peptides, 11 chains. Longest chain 11 peptides. Score 0.459 Round 5: 87 peptides, 13 chains. Longest chain 10 peptides. Score 0.452 Taking the results from Round 4 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3123 restraints for refining 1327 atoms. 2862 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3133 (Rfree = 0.000) for 1327 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.2614 (Rfree = 0.000) for 1312 atoms. Found 1 (6 requested) and removed 9 (3 requested) atoms. Cycle 8: After refmac, R = 0.2255 (Rfree = 0.000) for 1299 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 9: After refmac, R = 0.2207 (Rfree = 0.000) for 1287 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2128 (Rfree = 0.000) for 1281 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.59 Search for helices and strands: 0 residues in 0 chains, 1319 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1333 seeds are put forward Round 1: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.323 Round 2: 74 peptides, 10 chains. Longest chain 11 peptides. Score 0.456 Round 3: 82 peptides, 11 chains. Longest chain 17 peptides. Score 0.479 Round 4: 88 peptides, 12 chains. Longest chain 18 peptides. Score 0.489 Round 5: 88 peptides, 11 chains. Longest chain 14 peptides. Score 0.519 Taking the results from Round 5 Chains 11, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3217 restraints for refining 1370 atoms. 2920 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2876 (Rfree = 0.000) for 1370 atoms. Found 2 (6 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.2510 (Rfree = 0.000) for 1340 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 13: After refmac, R = 0.2313 (Rfree = 0.000) for 1326 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2412 (Rfree = 0.000) for 1317 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. Cycle 15: After refmac, R = 0.2150 (Rfree = 0.000) for 1308 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.61 Search for helices and strands: 0 residues in 0 chains, 1368 seeds are put forward NCS extension: 0 residues added, 1368 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 11 peptides. Score 0.290 Round 2: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.406 Round 3: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.362 Round 4: 76 peptides, 15 chains. Longest chain 7 peptides. Score 0.304 Round 5: 77 peptides, 12 chains. Longest chain 15 peptides. Score 0.412 Taking the results from Round 5 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3195 restraints for refining 1373 atoms. 2947 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2529 (Rfree = 0.000) for 1373 atoms. Found 3 (6 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.2420 (Rfree = 0.000) for 1356 atoms. Found 2 (6 requested) and removed 11 (3 requested) atoms. Cycle 18: After refmac, R = 0.2118 (Rfree = 0.000) for 1345 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.2041 (Rfree = 0.000) for 1337 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2090 (Rfree = 0.000) for 1334 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.65 Search for helices and strands: 0 residues in 0 chains, 1387 seeds are put forward NCS extension: 0 residues added, 1387 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 9 peptides. Score 0.263 Round 2: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.406 Round 3: 77 peptides, 14 chains. Longest chain 12 peptides. Score 0.346 Round 4: 81 peptides, 13 chains. Longest chain 12 peptides. Score 0.409 Round 5: 85 peptides, 14 chains. Longest chain 9 peptides. Score 0.406 Taking the results from Round 4 Chains 13, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3223 restraints for refining 1372 atoms. 2964 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2867 (Rfree = 0.000) for 1372 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 22: After refmac, R = 0.2410 (Rfree = 0.000) for 1360 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.2512 (Rfree = 0.000) for 1348 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2362 (Rfree = 0.000) for 1335 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2437 (Rfree = 0.000) for 1329 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.58 Search for helices and strands: 0 residues in 0 chains, 1371 seeds are put forward NCS extension: 0 residues added, 1371 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.239 Round 2: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.319 Round 3: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.294 Round 4: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.319 Round 5: 80 peptides, 12 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 5 Chains 12, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3222 restraints for refining 1364 atoms. 2962 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2592 (Rfree = 0.000) for 1364 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2296 (Rfree = 0.000) for 1355 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2442 (Rfree = 0.000) for 1343 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2075 (Rfree = 0.000) for 1338 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.2068 (Rfree = 0.000) for 1333 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 1375 seeds are put forward NCS extension: 0 residues added, 1375 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 7 peptides. Score 0.205 Round 2: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.331 Round 3: 67 peptides, 12 chains. Longest chain 10 peptides. Score 0.336 Round 4: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.351 Round 5: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.359 Taking the results from Round 5 Chains 12, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3277 restraints for refining 1373 atoms. 3057 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2473 (Rfree = 0.000) for 1373 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.1989 (Rfree = 0.000) for 1364 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.2138 (Rfree = 0.000) for 1364 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.1954 (Rfree = 0.000) for 1359 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1793 (Rfree = 0.000) for 1356 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.85 3.65 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward NCS extension: 0 residues added, 1392 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.256 Round 2: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.336 Round 3: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.382 Round 4: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.362 Round 5: 76 peptides, 13 chains. Longest chain 9 peptides. Score 0.372 Taking the results from Round 3 Chains 12, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3173 restraints for refining 1372 atoms. 2941 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2211 (Rfree = 0.000) for 1372 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.1969 (Rfree = 0.000) for 1361 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.1819 (Rfree = 0.000) for 1355 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.1809 (Rfree = 0.000) for 1352 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1912 (Rfree = 0.000) for 1348 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.63 Search for helices and strands: 0 residues in 0 chains, 1381 seeds are put forward NCS extension: 0 residues added, 1381 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.213 Round 2: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.297 Round 3: 73 peptides, 13 chains. Longest chain 8 peptides. Score 0.349 Round 4: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.362 Round 5: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.408 Taking the results from Round 5 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3259 restraints for refining 1373 atoms. 3026 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2160 (Rfree = 0.000) for 1373 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.2090 (Rfree = 0.000) for 1365 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2041 (Rfree = 0.000) for 1361 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1872 (Rfree = 0.000) for 1364 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1871 (Rfree = 0.000) for 1361 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.85 3.65 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward NCS extension: 0 residues added, 1403 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 13 peptides. Score 0.286 Round 2: 42 peptides, 6 chains. Longest chain 15 peptides. Score 0.353 Round 3: 47 peptides, 6 chains. Longest chain 15 peptides. Score 0.395 Round 4: 50 peptides, 6 chains. Longest chain 15 peptides. Score 0.418 Round 5: 42 peptides, 6 chains. Longest chain 12 peptides. Score 0.353 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pg4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2116 reflections ( 99.39 % complete ) and 3322 restraints for refining 1369 atoms. 3152 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2064 (Rfree = 0.000) for 1369 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1897 (Rfree = 0.000) for 1364 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1744 (Rfree = 0.000) for 1356 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1892 (Rfree = 0.000) for 1351 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:59 GMT 2018 Job finished. TimeTaking 28.01 Used memory is bytes: 7550416